1.2压缩算法

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已于 2022-04-21 16:13:21 修改

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分类专栏： Python_算法数算文章标签：压缩算法

于 2022-01-18 16:48:55 首次发布

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这里是使用Python对四种核苷酸（A、C、G、T）的压缩实现

class CompressedGene:
    def __init__(self,gene:str)->None:
        self._compress(gene)
    #压缩
    def _compress(self,gene:str)->None:
        self.bit_string:int=1
        for nuclleotide in gene.upper():
            self.bit_string<<=2 #左移两个单位
            if nuclleotide=="A":
                self.bit_string|=0b00
            elif nuclleotide=="C":
                self.bit_string|=0b01
            elif nuclleotide=="G":
                self.bit_string|=0b10
            elif nuclleotide=="T":
                self.bit_string|=0b11
            else:
                raise ValueError("无效核苷酸:{}".format(nuclleotide))
    #解压
    def decompress(self)->str:
        gene:str=""
        for i in range(0,self.bit_string.bit_length()-1,2):
            bits:int=self.bit_string>> i &0b11    #获取两个相关位
            if bits==0b00:
                gene+="A"
            elif bits==0b01:
                gene+="C"
            elif bits==0b10:
                gene+="G"
            elif bits==0b11:
                gene+="T"
            else:
                raise ValueError("无效位:{}".format(bits))
        return gene[::-1]   #逆序排列切片

    def __str__(self)->str:
        return self.decompress()

if __name__=="__main__":
    from sys import getsizeof
    original:str="TACGAAGTCAGTCATGCCCGAACTTGTACTGGAATACATGATCATGTCAGTCACGTGCTACGGGCTATATCAAAACGTCCTGCTTTATA"*100
    print("original is {}bytes".format(getsizeof(original)))#初始大小
    compressed: CompressedGene = CompressedGene(original)   #压缩
    print("compressed is {} bytes".format(getsizeof(compressed.bit_string)))
    print(compressed)   #解压(缩)
    print("original and decompressed are the same:{}".format(original==compressed.decompress()))